NucPred on Proteomes

Authors: Andrea Krings, Amine Heddad, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred - predictions for eukaryotic proteomes

Species:

Note: All filters/tests are combined with AND unless otherwise stated

Show only the proteins with links to database(s):
OMIM - human disease genes
PDB - protein 3D structure
( AND OR combination )

Annotation filters (can be slow! - Perl regexps allowed: e.g. nucleus|nucleolus)

UniProt ID (e.g. "PK3B_")
UniProt description (e.g. "kinase")
UniProt subcellular location
AND
UniProt GO component
AND
AND the
AND the

Only show proteins where the PredictNLS prediction is:

positive
negative

Only show proteins where the PSORT II predicted location

is is not

Click here: to filter by NucPred score

exclude all transmembrane proteins predicted by TMHMM
don't exclude lone N-terminal predicted transmembrane helices
(these could be signal peptides)

export all ACs and IDs as text file

Show proteins (ordered by NucPred score ) from to (currently 98716 matches)

You can bookmark/save your search criteria with this link. You can also start again with default settings.

UniProt accession	UniProt ID	UniProt description	NucPred score	Predict- NLS	PSORT II	TMHMM #helices	UniProt annotation for subcellular location	Uniprot GO cellular component	OMIM	PDB	sequence length
P00107 UniProt NPD GO	CYC6_PAVLU	Cytochrome c6 (Soluble cytochrome f) (Cytochrome c553) (Cytochrome c-553)	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid lumen				83
P00108 UniProt NPD GO	CYC6_PETFA	Cytochrome c6 (Soluble cytochrome f) (Cytochrome c553) (Cytochrome c-553)	0.01	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid lumen				85
P00111 UniProt NPD GO	CYC6_PORTE	Cytochrome c6 (Soluble cytochrome f) (Cytochrome c553) (Cytochrome c-553)	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid lumen (By similarity)				85
P57736 UniProt NPD GO	CYC6_SCEOB	Cytochrome c6 (Soluble cytochrome f) (Cytochrome c553) (Cytochrome c-553)	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid lumen			1C6R	89
Q9TLW1 UniProt NPD GO	CYC6_CYACA	Cytochrome c6 precursor (Soluble cytochrome f) (Cytochrome c553) (Cytochrome c-553)	0.01	-	mit	0	Plastid; chloroplast; chloroplast thylakoid lumen (By similarity)				109
Q8MTX2 UniProt NPD GO	TXT2_OPIMA	Cytotoxic linear peptide IsCT2 precursor [Contains: Cytotoxic linear peptide IsCT2f]	0.01	-	exc	1 *	Secreted protein				71
P01451 UniProt NPD GO	CX1_NAJOX	Cytotoxin 1	0.01	-	nuc	0	Secreted protein			1ZAD	60
P01455 UniProt NPD GO	CX1_NAJHA	Cytotoxin 1 (Toxin V-II-1)	0.01	-	nuc	0	Secreted protein				60
P01456 UniProt NPD GO	CX1_NAJNI	Cytotoxin 1 (Toxin V-II-1)	0.01	-	nuc	0	Secreted protein				60
P01453 UniProt NPD GO	CX10_NAJHA	Cytotoxin 10 (Toxin CM-4a)	0.01	-	nuc	0	Secreted protein				60
P01441 UniProt NPD GO	CX2_NAJOX	Cytotoxin 2 (CTII)	0.01	-	nuc	0	Secreted protein			1FFJ	60
P01440 UniProt NPD GO	CX2_NAJNA	Cytotoxin 2 (Cytotoxin II)	0.01	-	nuc	0	Secreted protein				60
P01462 UniProt NPD GO	CX2_NAJHA	Cytotoxin 2 (Toxin V-II-2/V-II-2A)	0.01	-	nuc	0	Secreted protein				60
P01459 UniProt NPD GO	CX3_NAJHA	Cytotoxin 3 (Toxin CM-8/CM-8A)	0.01	-	nuc	0	Secreted protein				60
P01461 UniProt NPD GO	CX4_NAJHA	Cytotoxin 4 (Toxin CM-11)	0.01	-	nuc	0	Secreted protein				60
P01443 UniProt NPD GO	CTX4_NAJAT	Cytotoxin 4 precursor (Cardiotoxin analog IV) (CTX-4) (CTX IV)	0.01	-	mit	0	Secreted protein			1KBT	81
P07525 UniProt NPD GO	CX5T_NAJAT	Cytotoxin 5 (Cardiotoxin analog V) (CTX-5) (CTX V) (Cardiotoxin T) (Cytotoxin D1) (Membrane toxin D1 ...	0.01	-	nuc	0	Secreted protein			1CHV	60
P01457 UniProt NPD GO	CX5_NAJHH	Cytotoxin 5 (Cytotoxin CM-8)	0.01	-	nuc	0	Secreted protein				60
P24779 UniProt NPD GO	CX5_NAJKA	Cytotoxin 5 (Cytotoxin II)	0.01	-	nuc	0	Secreted protein				60
P01464 UniProt NPD GO	CX5_NAJHA	Cytotoxin 5 (Toxin CM-6)	0.01	-	nuc	0	Secreted protein				60
P01465 UniProt NPD GO	CX6_NAJHA	Cytotoxin 6 (Toxin CM-2H)	0.01	-	nuc	0	Secreted protein				60
P01466 UniProt NPD GO	CX7_NAJHA	Cytotoxin 7 (Toxin CM-4B)	0.01	-	nuc	0	Secreted protein				60
P49122 UniProt NPD GO	CX7_NAJAT	Cytotoxin 7 precursor (Cardiotoxin 7) (CTX7) (Ctx-7)	0.01	-	mit	0	Secreted protein				82
P01460 UniProt NPD GO	CX8_NAJHA	Cytotoxin 8 (Toxin CM-7)	0.01	-	nuc	0	Secreted protein				60
P49123 UniProt NPD GO	CX8_NAJAT	Cytotoxin 8 precursor (Cardiotoxin 8) (CTX8)	0.01	-	mit	0	Secreted protein				81
P60308 UniProt NPD GO	CX5C_NAJAT	Cytotoxin SP15c	0.01	-	nuc	0	Secreted protein				60
P84193 UniProt NPD GO	AUD_PHACH	D-arabino-hex-2-ulose dehydratase (EC 4.2.1.-) (EC 5.-.-.-) (Aldos-2-ulose dehydratase) (Pyranosone ...	0.01	-	cyt	0					332
Q752Y3 UniProt NPD GO	ALO_ASHGO	D-arabinono-1,4-lactone oxidase (EC 1.1.3.37) (ALO) (L-galactono-gamma-lactone oxidase)	0.01	-	cyt	0	Mitochondrion; mitochondrial membrane (By similarity). Membrane-embedded (By similarity)				532
Q9HDX8 UniProt NPD GO	ALO_SCHPO	D-arabinono-1,4-lactone oxidase (EC 1.1.3.37) (ALO) (L-galactono-gamma-lactone oxidase)	0.01	-	mit	0	Mitochondrion; mitochondrial membrane (By similarity). Membrane-embedded (By similarity)				461
O35215 UniProt NPD GO	DOPD_MOUSE	D-dopachrome decarboxylase (EC 4.1.1.84) (D-dopachrome tautomerase)	0.01	-	cyt	0	Cytoplasm				117
P30046 UniProt NPD GO	DOPD_HUMAN	D-dopachrome decarboxylase (EC 4.1.1.84) (D-dopachrome tautomerase) (Phenylpyruvate tautomerase II)	0.01	-	cyt	0	Cytoplasm (By similarity)		602750	1DPT	117
Q8JIS3 UniProt NPD GO	DER_CHICK	D-erythrulose reductase (EC 1.1.1.162)	0.01	-	cyt	0	Cytoplasm				246
O14274 UniProt NPD GO	DTD_SCHPO	D-tyrosyl-tRNA(Tyr) deacylase (EC 3.1.-.-)	0.01	-	cyt	0	Cytoplasm (By similarity)				149
Q6C7S6 UniProt NPD GO	DTD_YARLI	D-tyrosyl-tRNA(Tyr) deacylase (EC 3.1.-.-)	0.01	-	mit	0	Cytoplasm (By similarity)				154
Q9DCP9 UniProt NPD GO	DAZP2_MOUSE	DAZ-associated protein 2 (Deleted in azoospermia-associated protein 2) (Proline-rich protein express ...	0.01	-	cyt	0		transcription factor complex [IC]			168
Q9HEU2 UniProt NPD GO	RAD59_KLULA	DNA repair protein RAD59	0.01	-	cyt	0	Nucleus (By similarity)				209
Q05212 UniProt NPD GO	DR102_ARATH	DNA-damage-repair/toleration protein DRT102	0.01	-	cyt	0					230
Q9Y535 UniProt NPD GO	RPC8_HUMAN	DNA-directed RNA polymerase III subunit 22.9 kDa polypeptide (EC 2.7.7.6) (RPC8)	0.01	-	cyt	0	Nucleus	DNA-directed RNA polymerase III complex [IDA] nucleoplasm [IDA]			204
Q9D2C6 UniProt NPD GO	RPC8_MOUSE	DNA-directed RNA polymerase III subunit 22.9 kDa polypeptide (EC 2.7.7.6) (RPC8)	0.01	-	cyt	0	Nucleus (By similarity)	DNA-directed RNA polymerase III complex [ISS] nucleoplasm [ISS]			204
P36441 UniProt NPD GO	RPOC1_HETCA	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.01	-	cyt	0	Plastid; chloroplast				33
P84269 UniProt NPD GO	DAH53_LITDA	Dahlein-5.3	0.01	-		0	Secreted protein	extracellular region [IDA]			20
P84271 UniProt NPD GO	DAH55_LITDA	Dahlein-5.5	0.01	-	cyt	0	Secreted protein	extracellular region [IDA]			21
P84272 UniProt NPD GO	DAH56_LITDA	Dahlein-5.6	0.01	-	cyt	0	Secreted protein	extracellular region [IDA]			21
Q9SMC4 UniProt NPD GO	DAD1_LYCES	Defender against cell death 1 (DAD-1)	0.01	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				116
O24060 UniProt NPD GO	DAD1_MALDO	Defender against cell death 1 (DAD-1)	0.01	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				119
O65085 UniProt NPD GO	DAD1_PICMA	Defender against cell death 1 (DAD-1)	0.01	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				115
Q9ZWQ7 UniProt NPD GO	DAD1_CITUN	Defender against cell death 1 (DAD-1) (CitDAD-1-1)	0.01	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				115
Q9ZRA3 UniProt NPD GO	DAD1_PEA	Defender against cell death 1 (DAD-1) (Peadad)	0.01	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				117
P37364 UniProt NPD GO	DEFI_PYRAP	Defensin	0.01	-	cyt	0	Secreted protein				43
Q43413 UniProt NPD GO	DEF1_CAPAN	Defensin J1-1 precursor	0.01	-	mit	1 *	Secreted protein				75

You are viewing entries 88001 to 88050 of 98716. You can see more proteins by changing the limits in the form at the top of this page, or click here for the next page of proteins .

If you find NucPred useful, please cite this paper:

NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022

The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold	Specificity	Sensitivity
see above	fraction of proteins predicted to be nuclear that actually are nuclear	fraction of true nuclear proteins that are predicted (coverage)
0.10	0.45	0.88
0.20	0.52	0.83
0.30	0.57	0.77
0.40	0.63	0.69
0.50	0.70	0.62
0.60	0.71	0.53
0.70	0.81	0.44
0.80	0.84	0.32
0.90	0.88	0.21
1.00	1.00	0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

Go back to the NucPred Home Page.